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Dectin-1 in complex with beta-glucan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BPE PDB ENTRY 2BPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 2M SODIUM CHLORIDE, 0.1M CITRIC ACID PH4.0, pH 4.00
Crystal Properties Matthews coefficient Solvent content 3.72 66.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.998 α = 90 b = 83.998 β = 90 c = 117.404 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH OSMIC 2005-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 50 100 0.24 18.4 31.4 12244 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 100 0.92 3.5 30.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BPE 2.8 72.74 11634 584 99.8 0.194 0.191 0.1886 0.245 10.22 RANDOM 45.26
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1 0.5 1 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.948 r_dihedral_angle_4_deg 21.281 r_dihedral_angle_3_deg 19.144 r_dihedral_angle_1_deg 7.168 r_scangle_it 3.807 r_scbond_it 2.326 r_mcangle_it 2.119 r_angle_refined_deg 1.836 r_mcbond_it 1.144 r_nbtor_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.948 r_dihedral_angle_4_deg 21.281 r_dihedral_angle_3_deg 19.144 r_dihedral_angle_1_deg 7.168 r_scangle_it 3.807 r_scbond_it 2.326 r_mcangle_it 2.119 r_angle_refined_deg 1.836 r_mcbond_it 1.144 r_nbtor_refined 0.331 r_symmetry_vdw_refined 0.294 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.117 r_symmetry_hbond_refined 0.071 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2086 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing